1 changed files with 3 additions and 3 deletions
+ 3
- 3
tasks/pathseq.wdl
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| -O ./ubam/${sample_id}.bam \ | -O ./ubam/${sample_id}.bam \ | ||||
| -SM ${sample_id} | -SM ${sample_id} | ||||
| time gatk --java-options "-Xmx110g" PathSeqFilterSpark \ | |||||
| time gatk --java-options "-Xmx185g" PathSeqFilterSpark \ | |||||
| --input ./ubam/${sample_id}.bam \ | --input ./ubam/${sample_id}.bam \ | ||||
| --paired-output ./clean_pair_bam/${sample_id}_paired.bam \ | --paired-output ./clean_pair_bam/${sample_id}_paired.bam \ | ||||
| --unpaired-output ./clean_unpaired_bam/${sample_id}_unpaired.bam \ | --unpaired-output ./clean_unpaired_bam/${sample_id}_unpaired.bam \ | ||||
| --filter-bwa-image ${host_image} \ | --filter-bwa-image ${host_image} \ | ||||
| --filter-metrics filter_log/${sample_id}.log | --filter-metrics filter_log/${sample_id}.log | ||||
| time gatk --java-options "-Xmx110g" PathSeqBwaSpark \ | |||||
| time gatk --java-options "-Xmx185g" PathSeqBwaSpark \ | |||||
| --paired-input ./clean_pair_bam/${sample_id}_paired.bam \ | --paired-input ./clean_pair_bam/${sample_id}_paired.bam \ | ||||
| --unpaired-input ./clean_unpaired_bam/${sample_id}_unpaired.bam \ | --unpaired-input ./clean_unpaired_bam/${sample_id}_unpaired.bam \ | ||||
| --paired-output bwa_pair_bam/${sample_id}_bwa_paired.bam \ | --paired-output bwa_pair_bam/${sample_id}_bwa_paired.bam \ | ||||
| --microbe-dict ${microbe_dict} | --microbe-dict ${microbe_dict} | ||||
| time gatk --java-options "-Xmx110g" PathSeqScoreSpark \ | |||||
| time gatk --java-options "-Xmx185g" PathSeqScoreSpark \ | |||||
| --paired-input bwa_pair_bam/${sample_id}_bwa_paired.bam \ | --paired-input bwa_pair_bam/${sample_id}_bwa_paired.bam \ | ||||
| --unpaired-input bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \ | --unpaired-input bwa_unpair_bam/${sample_id}_bwa_unpaired.bam \ | ||||
| --taxonomy-file ${microbe_taxonomy} \ | --taxonomy-file ${microbe_taxonomy} \ |
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